NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees

Chen, Kevin C.; Durand, Dannie; Farach-Colton, Martı́n

doi:10.1089/106652700750050871

Cited by 506 publications

(471 citation statements)

References 27 publications

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“…Extensions to non-binary gene or species trees have been developed [33,114], as well as extensions to unrooted trees [33]. Moreover, all the following developments can be directly generalized to the reconciliation of a forest of gene trees.…”

Section: Reconciliation: Gene Family Evolution By Duplication Speciamentioning

confidence: 99%

“…For this reason, appropriate optimization criteria, either combinatorial or probabilistic [5], should be considered. The combinatorial criteria most often considered in the literature are the number of duplications (duplication cost), the number of losses (loss cost), or both (mutation cost) [33,77].…”

Section: Optimization Criteriamentioning

confidence: 99%

“…The problem is to infer, from the set of gene trees, a species tree S leading to a parsimonious evolution scenario, for a chosen cost. As in the case of a known species tree, methods have been developed for the duplication and mutation cost versions of this problem [33,59,77]. For both criteria, inference of an optimal species tree given a forest of gene trees is an NP-hard problem [77].…”

Section: Algorithmsmentioning

confidence: 99%

“…Another strategy adopted in [33] is to explore the space of gene trees obtained from the original gene tree T by performing Nearest Neighbor Interchanges (NNI's) around weakly-supported edges. The problem is then to select, from this space, the tree giving rise to the minimum reconciliation cost.…”

Section: Noise In Gene Treesmentioning

confidence: 99%

See 3 more Smart Citations

Analysis of Gene Order Evolution Beyond Single-Copy Genes

El-Mabrouk

Sankoff

2012

Methods in Molecular Biology

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The purpose of this chapter is to provide a comprehensive review of the field of genome rearrangement, i.e., comparative genomics based on representation of genomes as ordered sequences of signed genes. We specifically focus on the "hard part" of genome rearrangement, how to handle duplicated genes. The main questions are: how have present-day genomes evolved from a common ancestor? What are the most realistic evolutionary scenarios explaining the observed gene orders? What was the content and structure of ancestral genomes? We aim to provide a concise but complete overview of the field, starting with the practical problem of finding an appropriate representation of a genome as a sequence of ordered genes or blocks, namely the problems of orthology, paralogy and synteny block identification. We then consider three levels of gene organization: the gene family level (evolution by duplication, loss and speciation), the cluster level (evolution by tandem duplications) and the genome level (all types of rearrangement events, including whole genome duplication).

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Section: Reconciliation: Gene Family Evolution By Duplication Speciamentioning

confidence: 99%

Section: Optimization Criteriamentioning

confidence: 99%

Section: Algorithmsmentioning

confidence: 99%

Section: Noise In Gene Treesmentioning

confidence: 99%

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Analysis of Gene Order Evolution Beyond Single-Copy Genes

El-Mabrouk

Sankoff

2012

Methods in Molecular Biology

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“…A duplication and loss history for the gene family is then directly deduced from R. As many reconciliations exist, a natural approach is to select the one that optimizes a given criterion. Natural combinatorial criteria are the number of duplications (duplication cost), losses (loss cost) or both combined (mutation cost) [6,20]. The so called Lowest Common Ancestor (LCA) mapping between a gene tree and a species tree, formulated in [15,24] and widely used [3,10,14,20,[22][23][24], defines a reconciliation that minimizes both the duplication and mutation costs.…”

Section: Introductionmentioning

confidence: 99%

Removing Noise from Gene Trees

Doroftei¹,

El-Mabrouk²

2011

Lecture Notes in Computer Science

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Abstract. Reconciliation is the commonly used method for inferring the evolutionary scenario for a gene family. It consists in "embedding" an inferred gene tree into a known species tree, revealing the evolution of the gene family by duplications and losses. The main complaint about reconciliation is that the inferred evolutionary scenario is strongly dependant on the considered gene tree, as few misplaced leaves may lead to a completely different history, with significantly more duplications and losses. As using different phylogenetic methods with different parameters may lead to different gene trees, it is essential to have criteria to choose, among those, the appropriate one for reconciliation. In this paper, following the conclusion of a previous paper, we flag certain duplication vertices of a gene tree, the "non-apparent duplication" (NAD) vertices, as resulting from the misplacement of leaves, and consider the optimization problem of removing the minimum number of leaves leading to a tree without any NAD vertex. We develop a polynomial-time algorithm that is exact for two special classes of gene trees, and show a good performance on simulated data sets in the general case.

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Tracing the evolution of fatty acid‐binding proteins (FABPs) in organisms with a heterogeneous fat distribution

Zhang

Ren

et al. 2020

FEBS Open Bio

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The distribution of fat among both invertebrate and vertebrate groups is heterogeneous. Studies have shown that fatty acid‐binding proteins (FABPs), which mainly bind and transport fatty acids, play important roles in the regulation of fat storage and distribution. However, the systematic and genome‐wide investigation of FABP genes in organisms with a heterogeneous fat distribution remains in its infancy. The availability of the complete genomes of Caenorhabditis elegans, Callorhinchus milii, and other organisms with a heterogeneous fat distribution allowed us to systematically investigate the gene structure and phylogeny of FABP genes across a wide range of phyla. In this study, we analyzed the number, structure, chromosomal location, and phylogeny of FABP genes in 18 organisms from C. elegans to Homo sapiens. A total of 12 types of FABP genes were identified in the 18 species, and no single organism exhibited all 12 fatty acid‐binding genes (FABPs). The absence of a specific FABP gene in tissue may be related to the absence of fat storage in the corresponding tissue. The genomic loci of the FABP genes were diverse, and their gene structures varied. The results of the phylogenetic analysis and the observation of conserved gene synthesis of FABP family genes/proteins suggest that all FABP genes may have evolved from a common ancestor through tandem duplication. This study not only lays a strong theoretical foundation for the study of fat deposition in different organisms, but also provides a new perspective regarding metabolic disease prevention and control and the improvement of agricultural product quality.

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NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees

Cited by 506 publications

References 27 publications

Analysis of Gene Order Evolution Beyond Single-Copy Genes

Analysis of Gene Order Evolution Beyond Single-Copy Genes

Removing Noise from Gene Trees

Tracing the evolution of fatty acid‐binding proteins (FABPs) in organisms with a heterogeneous fat distribution

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